The following problems occurred while reading PDB file for CCNE1_minimized.pdb
warning: cannot find LINK/SSBOND residue TPO (160 )
warning: cannot find LINK/SSBOND residue TPO (160 )
#0, chain A: cyclin-dependent kinase 2
#0, chain B: G1/S-specific cyclin-E1
The following problems occurred while reading PDB file for C10_CCNE1_DOCK.pdb
warning:  Ignored bad PDB record found on line 1
warning:  Ignored bad PDB record found on line 2
warning:  Ignored bad PDB record found on line 3
warning:  Ignored bad PDB record found on line 4
warning:  Ignored bad PDB record found on line 5
warning:  Ignored bad PDB record found on line 6
warning:  Ignored bad PDB record found on line 7
warning:  Ignored bad PDB record found on line 8
warning:  Ignored bad PDB record found on line 9
warning:  Ignored bad PDB record found on line 10
Suppressed 3 warnings about bad PDB records
No incomplete side chains
Terminii for CCNE1_minimized.pdb (#0) chain A determined from SEQRES records
Terminii for CCNE1_minimized.pdb (#0) chain B determined from SEQRES records
Chain-initial residues that are actual N terminii: #0 SER 0.A
Chain-initial residues that are not actual N terminii: #0 HIS 161.A, #0 SER 88.B
Chain-final residues that are actual C terminii: 
Chain-final residues that are not actual C terminii: #0 TYR 159.A, #0 ARG 297.A, #0 LYS 357.B
539 hydrogen bonds
Removing spurious proton from 'C' of #0 TYR 159.A
Removing spurious proton from 'C' of #0 ARG 297.A
Removing spurious proton from 'C' of #0 LYS 357.B
Hydrogens added
Charge model: AMBER ff14SB
Assigning partial charges to residue C10 (net charge +0) with am1-bcc method
Running ANTECHAMBER command: D:/docking/Chimera 1.14/bin/amber18/bin\antechamber -ek qm_theory='AM1', -i c:\users\萌\appdata\local\temp\tmptnfud6\ante.in.mol2 -fi mol2 -o c:\users\萌\appdata\local\temp\tmptnfud6\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(C10) 

(C10) Welcome to antechamber 17.3: molecular input file processor.

(C10) 

(C10) Info: Finished reading file (c:\users\萌\appdata\local\temp\tmptnfud6\ante.in.mol2).

(C10) Running: "D:/docking/Chimera 1.14/bin/amber18/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(C10) 

(C10) 

(C10) Running: "D:/docking/Chimera 1.14/bin/amber18/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(C10) Info: Total number of electrons: 266; net charge: 0

(C10) 

(C10) Running: "D:/docking/Chimera 1.14/bin/amber18/bin/sqm" -O -i sqm.in -o sqm.out

(C10) 

(C10) Running: "D:/docking/Chimera 1.14/bin/amber18/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "D:/docking/Chimera 1.14/bin/amber18/dat/antechamber/BCCPARM.DAT" -s 2 -j 1

(C10) 

(C10) Running: "D:/docking/Chimera 1.14/bin/amber18/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

(C10) 

Charges for residue C10 determined
Total charge for #0: 13.000
Total charge for #1: 0.001
Running PARMCHK for C10_CCNE1_DOCK.pdb
command: D:/docking/Chimera 1.14/bin/amber18/bin\parmchk2 -i c:\users\萌\appdata\local\temp\tmp6x9yql\parmchk.in.1-0 -f mol2 -o c:\users\萌\appdata\local\temp\tmp6x9yql\frcmod.1-0 -p D:/docking/Chimera 1.14/bin/amber18\dat\leap\parm\gaff.dat
Finished PARMCHK for C10_CCNE1_DOCK.pdb
IOError Exception in Tk callback
  Function: <function command at 0x0000000015438748> (type: <type 'function'>)
  Module: <module 'chimera.baseDialog' from 'D:\docking\Chimera 1.14\share\chimera\baseDialog.pyc'> (line: 447)
  Args: ()
Traceback (innermost last):
  File "D:\docking\Chimera 1.14\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
  File "D:\docking\Chimera 1.14\share\chimera\baseDialog.py", line 449, in command
    getattr(s, buttonFuncName(txt))()
  File "D:\docking\Chimera 1.14\share\chimera\baseDialog.py", line 704, in OK
    self.Apply()
  File "D:\docking\Chimera 1.14\share\AddCharge\gui.py", line 172, in Apply
    self.cb(self.unchargedResidues, self.unchargedAtoms)
  File "D:\docking\Chimera 1.14\share\AddCharge\__init__.py", line 127, in doneCB
    cb(ur, ua)
  File "D:\docking\Chimera 1.14\share\DockPrep\__init__.py", line 303, in <lambda>
    _chargeCB(ur, uc, m, **kw))
  File "D:\docking\Chimera 1.14\share\DockPrep\__init__.py", line 308, in _chargeCB
    _postAddCharge(mols, **kw)
  File "D:\docking\Chimera 1.14\share\DockPrep\__init__.py", line 319, in _postAddCharge
    doneCB()
  File "D:\docking\Chimera 1.14\share\MMMD\MMTKinter.py", line 143, in _finishDockPrep
    self._finishInit()
  File "D:\docking\Chimera 1.14\share\MMMD\MMTKinter.py", line 59, in _finishInit
    self._makeUniverse()
  File "D:\docking\Chimera 1.14\share\MMMD\MMTKinter.py", line 90, in _makeUniverse
    parameters = readAmber99(os.path.join(paramDir, "gaff.dat"), modFiles)
  File "D:\docking\Chimera 1.14\bin\lib\site-packages\MMTK\ForceFields\Amber\AmberForceField.py", line 143, in readAmber99
    params = AmberData.AmberParameters(main_file, mod_files)
  File "D:\docking\Chimera 1.14\bin\lib\site-packages\MMTK\ForceFields\Amber\AmberData.py", line 83, in __init__
    file = TextFile(mod)
  File "D:\docking\Chimera 1.14\bin\lib\site-packages\Scientific\IO\TextFile.py", line 61, in __init__
    + filename))
IOError: (2, 'No such file or directory: D:\\docking\\Chimera 1.14\\bin\\lib\\site-packages\\MMTK\\ForceFields\\Amber\\frcmod.1-0')

IOError: (2, 'No such file or directory: D:\\docking\\Chimera 1.14\\bin\\lib\\site-packages\\MMTK\\ForceFields\\Amber\\frcmod.1-0')

  File "D:\docking\Chimera 1.14\bin\lib\site-packages\Scientific\IO\TextFile.py", line 61, in __init__
    + filename))

See reply log for Python traceback.


Exception AttributeError: "TextFile instance has no attribute 'file'" in <bound method TextFile.__del__ of <Scientific.IO.TextFile.TextFile instance at 0x000000001799F148>> ignored